Not Really The End
by CUBSsquint
Summary: This story starts off right where the finale left off. Feel free to message me suggestions or comments
1. Separation

They had held hands. They said good-bye, and walked off. Both turned, each waiting for the other to make an advance, but neither did. So off they went, their separate directions, not completely sure if they'd return safe to see each other again.

* * *

Brennan walked back to the others, grabbed her bags, and joined Daisy to board the plane. In the back of her mind she half expected Booth to come grabbing her arm at any moment.

"Are you alright Dr. Brennan?" Daisy asked, slightly confused at her mentor's behavior, "Aren't you excited for the finds at the Maluku islands?"

"Hmm, yes Miss Wick, I'm fine. Shouldn't you have your boarding pass out?"

"Oh yes Dr. Brennan." Daisy rummaged around in her carry-on and pulled out the crumpled piece of paper.

They boarded the plane and took their seats in silence. In first class, Brennan sat by the window with the empty seat besides her. She was reminded of her trip to China to look at ancient bones which had been halted due to the murder on her plane. Booth had snuck up from his seat to sit next to her, making goofy noises, and had been sent back to coach despite flashing his FBI badge.

She took out the brief she had been sent on the discoveries, and occupied herself by reading all information that could advance her knowledge on the specimens for when they arrived. But there was still something nagging in the back of her mind.

* * *

Booth had been so tempted to hold her, to kiss her, to make sure she knew he'd wait, but still he was afraid she wasn't ready. Still reminded of his failed attempt, he had been unsure how to handle their separation. One year was a long time, three-hundred and sixty-five days to be exact, the same amount of time they spent apart after their first kiss… and first rejection. Maybe it just wasn't meant to be, but he felt that someday she'd come around. He knew it, that in thirty, forty, or fifty years he'd be the one. He'd be her guy. But how long he could wait was a question he didn't have the answer to.

Back on base Booth prepared to be sent to Afghanistan. His mind was filled with painful memories from his army days and of Corporal Parker's death. He knew that by going he was preventing more deaths, a way of repaying Teddy's untimely death.

As his plane took off, Booth looked down over the mall. He saw the reflecting pool across from the Lincoln Memorial. "One year," he said to himself, "One long year."


	2. Heading Home

-ONE YEAR LATER-

Time went slowly. But soon enough the days passed by.

* * *

Temperance Brennan began packing to leave the Maluku Islands. She and Miss Wick had contributed greatly to a discovery that will impact the way science and history are studied forever. She was very eager to get home and publish her findings.

Lately she had been a bit depressed though, very anxious to get back home. Daisy, rather gloomy and less talkative at the start of the trip, was now…

"Oh Lancelot!"

…happily reunited with Dr. Sweets, who had recently joined them for their last week in Maluku. They reunited and the engagement was immediately back on. While the two of them were spending time reconciling Brennan had felt very much alone and had a lot of time to think about things. She still didn't know what to expect when she got back to D.C.

* * *

Booth was ready to go home. The army had too much heart-break, while not as sad as some murder cases, hearing that young men whom he had just trained had already lost their lives was starting to take its toll on him.

He wanted to go back home, to Parker and to…Bones. He had no idea what her feelings towards him would be. Would absence make the heart grow fonder? Or would she still not be interested. Or worse, would she be bringing someone back from the Mai-poo-poo islands? He quickly put that idea out of his mind.

His bags were packed, and he ran off to catch his flight home.


	3. Surprises

"Sweetie!"

Brennan looked around to see where the familiar voice had come from. "Oh Angela! Hodgins!" She said when she saw her friends just around the corner. They walked quickly towards each other, quickly exchanging hugs.

"Oh my gosh, Ang! You're pregnant!" Brennan squealed.

"Wha…sweetie how'd you know!" Angela exclaimed.

"Your gait, your bones already show it as you walk. This is amazing Angela!"

"Aww, way to ruin our surprise. But thanks! I'm two months along. Isn't this so exciting!" Angela said as Hodgins put his arm lovingly around her.

"This is great! Congratulations!" Brennan replied, "Everything's changing, and it looks as if things are changing for the better."

"Let's get you home Bren, you look exhausted. So did you find something that changes life as we know it?" Angela said as they grabbed Brennan's luggage and began walked towards the parking garage.

"Well it won't change life, because this is a concept about the past, but it will present a new theory to how present life came to be. It's very fascinating; you'll have to read the article I'm preparing for the National Anthropology Journal."

"Of course we'll read it Dr. Brennan," said Hodgins, "But where's Daisy?"

"Oh, didn't you know? Dr. Sweets came to the Maluku islands last week and reunited with Miss Wick. The two of them decided to elope and honeymoon around the world for a few months before returning to work."

"Whoa." Angela said while Hodgins looked equally shocked, "Hmm, but still, I kind of saw that one coming, you know."

"Yes well," Brennan said, "When does Booth get back?"

"I was wondering why you hadn't asked that sooner," Hodgins smirked, "But haven't you been in contact with him?"

Brennan looked upset. "Yes well, we emailed a bit at the beginning, but we were both so busy and the internet connection was poor, and…"

Angela cut her off, "Booth's flight gets in tomorrow sweetie. So right now let's get you home so you can get some sleep."

"Yes alright," Brennan replied, "And thanks, you guys, you really didn't have to pick me up at the airport."

"No problem Dr. B." Hodgins said as the three of them got into the car.

It took about a half hour to get to Brennan's house, but the car was never silent, as they all had much to tell of the previous year.

When they arrived, they could see a light on in her window.

"Uhm, there's someone in your house?" Angela asked.

"I don't know who that would be?" Brennan replied.

"I'll come with you to the door, just to be safe. Angela you stay here." Hodgins said.

"Ugh, being pregnant gets you left out of all the fun. Alright, be safe. I hope it's not some big scary bad guy, I mean after all you just got home."

Hodgins and Brennan walked up the stairs to her apartment. Brennan went to knock on the door.

"Wait, shouldn't I do that?" Hodgins quickly said.

"Why, because you're supposedly the dominant male in this situation? I don't think it's a threatening situation so it shouldn't affect you manliness if I were to knock on the door." Brennan stated to a slightly confused Hodgins.

As Brennan stopped talking the door flew open. "Hey there!" said a familiar voice.

"Dad!" Brennan cried, and quickly hugged her father.

"Alright, I'm not really needed here and Angela will be worried in the car. Night Dr. Brennan. Good to see you Max." Hodgins said.

"Thanks Hodgins," Brennan said as he headed down the stairs. Then she turned to her father, "Dad! What are you doing here; it's the middle of the night?"

"Well I heard you were getting back today, and I figured you're friends would be picking you up from the airport, so I thought I'd surprise you at home." Max grinned, "And just so you know, you should have at least called me before you flew half-way around the world. An email when you're already gone isn't really enough for a concerned father."

"Sorry dad! I was just so excited. It was an amazing find, I've already begun writing my paper for the journal on it." Brennan said in a slightly apologetic tone.

"No worries," Max said, "Your brother told me to say hi for him and the girls. Did he tell you that he's married now?"

"What? No I hadn't heard. That is great, he'll be a good father for those little girls."

"Yes he better be," said Max in his slightly threatening but always caring voice, "Now honey, tell me all about your little scientific adventure. Did Booth go with you?"

"No Dad he didn't"

"What, why not? I don't think I've ever seen him not by your side."

"He went to Afghanistan to train soldiers for the army."

"For a year too? That's a long time for you two to be apart…"

"Dad, what are you implying?"

"Well it's, hmm, never mind. When does Booth get back?" Max asked.

"Tomorrow!" Brennan said a little too eagerly, which Max seemed to notice because he simply smiled and dropped the subject.

"You must be awfully tired, off to bed now." Max said, "I put new sheets on for you and I've already turned on the air conditioning, it was over a hundred degrees when I got here."

"Thanks dad. Good-night," Brennan said as she went off to get ready for bed. She was still very anxious for tomorrow.


	4. Doubts

She hadn't been able to sleep. She had woken up a few times during the night and was yelled at for turning on the lights by her father sleeping on the couch. She was just too nervous.

Finally after getting a few straight hours of sleep, Brennan woke up at nine am that morning. She contemplated going to meet Booth's flight at the airport, surprising him instead of going to their planned meeting spot, but even so that wasn't for about six more hours.

She decided to stop by the Jeffersonian to see when she could start back at work.

"Cam!" she said to the first familiar face she saw when she arrived there.

"Dr. Brennan!" Cam exclaimed, "I did not know you were back yet. So how were the Maluku islands?"

"Great Dr. Saroyan," Brennan replied, "You'll be able to read all about in the journal later. So when can I start back at work."

"Oh well, glad you had a good time," Cam said as she usually says whenever she gets an unexpected answer from Brennan, "You can start back whenever you like. I'd like you to meet your 'replacement' first."

"Uhm, alright?" Brennan replied.

"Dr. Brennan!" a voice screamed.

"No…" Brennan said in disbelief, "Zack!" she called out.

"Yes," replied the familiar boyish scientist now walking down from the forensics platform, "You look surprised?"

"Zack!" Brennan yelped, "They finally let you out?" She quickly hugged her favored intern.

"Yes. They did," Zack said happily, "With the suggestions from Dr. Saroyan and the others I was able to work back here as your replacement despite the slight detainment."

"Yes," Cam added, "And now that you're back, Zacky's going to get to stay with us as a full-fledged doctor in his own right. After all, he finished his dissertation."

"This is wonderful!" Brennan said, thinking of how many times already she'd used that exclamation. Truly, everything was changing, but some things seemed to be falling back in place, at least until…

"Temperance?" a familiar voice called out. Brennan turned, and was utterly speechless. Before her stood someone she had not thought she'd ever see again, someone she did kind of miss, someone who was causing her incredible conflict of emotions.

"Sully?" Brennan asked.

"Hey Temperance!" Sully said as he ran up and gave her a hug, "I haven't seen you in forever!"

"Sully, what…" Brennan was confused, "Sully what are you doing here?"

"I heard they needed someone to fill in for Booth for a year, and I thought 'hey I've already had some experience working over there so why not'?" Sully said eagerly, "It's been too long since I've seen you" He said, wrapping his arms around her, drawing her into another hug.

But Brennan, while excited and shocked, was confused. "You were supposed to be back a few years ago!"

"Well, I spent more time on the boat than expected. After I did get back I didn't really have the courage to come talk to you, and when I did, I found out that you were gone for a year, and that's when I learned about the vacant FBI spot at the Jeffersonian." Sully explained.

"This is great," Brennan said, although she was being torn apart inside. Why would it be that when she finally thought she had it all figured out with Booth (she had already decided of a certain something she was going to tell him later), that one of the only other guys she'd been in a serious relationship with would show up in her life again.

Cam must've noticed Brennan's internal struggle, because she then called out, "Dr. Brennan, sorry to interrupt but can we go to your office to discuss when you can return to work?"

Relieved, Brennan replied, "Yes Dr. Saroyan, I'll be there right away," and then to Sully, "I'll see you in a little bit."

"Yes. Good to see you Temperance," Sully said, letting go of his friendly grip on her arm as Brennan hurried off to her office.

"Why?" She said out loud when she was finally alone with Cam.

"I'm assuming you're talking about Sully being back and not asking why I called you to your office," Cam said.

"Yes, I-" Brennan started, "I-, but Booth-, but I don't know."

"Dr. Brennan it may not be my place but…" Cam started, "Oh wait, Angela's here, let me go get her really quick!" She hurried out of the room to get some help on advising the emotionally confused Dr. Brennan. "Angela!" She called out.

"Whoa, yes Cam?" Angela asked, "What's wrong?"

"Well, as you might have noticed we hired Sully as a replacement, and, uh, Brennan is in need of advise in her office" Cam responded.

"Oh no," Angela said, "I was hoping things were going to finally work out with Booth. I mean, Sully's a great guy and everything, but her and Booth…"

"I know," Cam said, "So come help me."

They both hurried back to Brennan's office.

"Sweetie, are you alright?" Angela asked.

"Huh, Ang?" Brennan said as she looked up from her desk.

"Aww have you been crying!" Angela asked as she hurried to hug and consol her friend.

"No I haven't," Brennan lied, "I'm just…confused" she admitted.

"I'm sorry," Cam said, "Sully applied, and he only wanted to stay for a year, so I figured it was an easy way to hold Booth's spot. I didn't think of this."

"What should I do," Brennan asked.

"Sweetie, what were you planning on telling Booth?" Angela asked gently, "Just because you've run into an old boyfriend shouldn't change anything."

"Well, I was going to tell him…" Brennan started, "But seeing Sully…"

"I know it could seem complicated, but really this shouldn't change things for you," Cam said.

"Yes, what were you going to tell Booth?" Angela added.

"I was going to tell him…" Brennan couldn't seem to admit it, "Well, after Sweets' book came out, with its conclusion…"

Angela and Cam looked at each other knowingly.

"Booth told me," Brennan continued, "that he…loved me. But I couldn't, I just couldn't, I didn't think I could change. But this past year I've been thinking and…"

"He loves you! You love him!" Angela screamed, "Ah, I've always known sweetie, it's about time that you realized it too."

"Sully definitely should not change anything," Cam said, "You've obviously thought this over a lot the past year, and it would seem trivial to not pursue it because of him."

"Well, I guess I…" Brennan began, starting to look a tad more cheerful.

"Come on, let's get you to the airport," Angela said, "Once you see Booth all hot in that army uniform again you won't be having doubts."


	5. Reunited

They checked the arrivals board and saw that Booth's flight was due in about ten minutes, so they took a seat. Angela couldn't help noticing how nervous her friend was, but she herself was excited. Finally Brennan and Booth could get together, six years was way too long of a wait.

"Flight 216 from Afghanistan is arriving now," a voice over the loud speaker said.

"You ready sweetie?" Angela asked Brennan.

"Wha-, yes," Brennan answered, seeming distracted.

Then Angela saw Booth walking out with the crowd of people. He was talking to another guy in the same army gear. 'Uh-oh,' she thought to herself when she saw a woman pushing her way from behind the crowd to get to the guys. Quickly, Angela tried to distract Brennan, but that didn't work. To her relief, the woman was soon tugging on the arm of the man Booth was talking to, not Booth's. "Bren, there he is," she said, once there was no longer any possibly threat.

"Booth!" Brennan yelled as she jumped out of her seat to go to him.

"Bones!" he called back equally excited, "What are you doing at the airport?" he grinned.

"Well I heard you got back today…" Brennan explained as they were awkwardly surrounded by the reunions of other couples, who were hugging and kissing their recently arrived loved ones.

"Oh, when'd you get back?" Booth asked curiously.

"Yesterday," she said.

Angela sense their conversation was getting a bit awkward and that now was the perfect time to butt in. "Booth! Welcome back," she said, making her way towards them.

"Hey Angela," he said, "How was your year in Paris?"

"Fantabulous," she said, "You'll never guess…"

"She's pregnant!" Brennan interrupted.

"Really, sweetie? Ruin my surprise again?" Angela said laughing.

"Whoa, that's so great!" Booth said giving Angela a hug.

"Why thanks," Angela said, "And dang, you are a good hugger," she said winking at Brennan. "Well how about I take your things back to the Jeffersonian and you two get that cup of coffee you had planned on."

"Alright," Booth said grinning, "How 'bout it?" he asked Brennan.

"Sounds good," she smiled.

Booth handed Angela his bag, grabbed Brennan's hand, and they walked off. Angela just stood there grinning. 'If something's not going on there…' she thought to herself.


	6. Puppydog Face

They had gone to "their" coffee cart on the mall in relative silence. They were happy to be back in each other's presence again, but there was something…wrong, just something seemed…out of place.

"So Bones, how were the Mai-poo-poo islands?" Booth asked breaking the silence once they were sitting on the bench drinking their coffee.

"Maluku. It was great Booth, so many fascinating scientific discoveries!" She didn't go into detail though; she understood she could be a bit dull at times. "Did it feel good to go back to the army?"

"Yes, well…it's just good to be home," Booth said. He then turned and stared directly into her eyes, "I've missed you Bones."

Brennan, startled, broke the eye contact. "It's been a long time since I've been called that."

After another slight silence, Booth said, "Remember when you said that if we didn't work together we wouldn't even have coffee?"

"What? I never said…" Brennan said.

"Yes you did, during our first few therapy sessions with Sweets."

"Oh that. But in your situation we never would've met, and…"

Booth cut her off. "I'm just saying this is nice."

"Yes, but we will be working together soon," and there went Brennan, ruining a potentially sweet moment by being serious, "My replacement was Zack! He's going to get his own position when I return. And your replacement was Sully…"

"What? Sully?" Booth practically yelped. The last thing he needed right now was Sully coming and taking Brennan away from him again.

"Yes Sully," Brennan said a bit nervously, "He only wanted to stay for the year so Cam figured he was the perfect guy to hold your spot." She could still see that he was tense and it worried her. But she still couldn't shut that big mouth of hers, and part of her wanted to see if he'd get jealous. "He was quite glad to see me," she said.

Booth didn't say anything, just looked down with his hurt puppy dog face. Then he said, "I guess it's nice for you to see him again."

'What?' Brennan thought. She had expected him to be jealous, not to give up this easily. She was starting to feel mad at him, but she didn't really know why. "I guess," she finally said.

"You know, I really ought to go see Parker," Booth said, "I'll swing by the Jeffersonian later to get my stuff. See ya, Bones." And with that, he was gone. Brennan was about to say something, but didn't know what to say. As she watched him walk away she was tempted to run after him.

But Brennan just sat there confused. She had expected a bit of jealousy, but not the beat-up sad puppy dog look. It had almost been more than she could take. But his abrupt leaving left her miserable. Maybe he had changed more this past year. Maybe he just couldn't take anymore of the heartbreak with her. She still couldn't understand her feelings. She'd probably have to talk to Angela. It'd be best to just head back to the Jeffersonian and hope to see Booth later.


	7. Goodbye

Back at the Jeffersonian Brennan sulked in her office. She then heard a knock on the door, and looked up to see Sully.

He walked in. "Hey Temperance, I was wondering if you wanted to get some coffee or something, have some time to catch up on things." He asked.

Brennan didn't know what to do. She wanted to talk with him, but as an old friend, which isn't what Sully seemed to have in mind. She also knew that if anything were to start up again with him she'd never have a chance of being with Booth. "Sorry Sully, I'm kind of busy here," she lied, "A lot of paper work, I've been gone for quite a while."

"Alright," he smiled, "Some other time." And he walked out of her office, and was immediately cornered by Angela.

"Come here," Angela said, leading him away from Brennan's office.

"What's going on?" Sully asked.

"I need to talk to you," Angela said. "Okay, here's the deal. You need to leave Brennan alone."

"What?" Sully asked.

"Yes, okay I'm sorry. You're a nice guy and all but there's a problem."

"What's the problem?" Sully was really confused.

"Well Booth loves Brennan." Angela said.

"Oh, I'd sort of realized that before…but he said he was fine with me dating Temperance last time?" Sully said.

"Well…no he wasn't. So the problem is that Booth's told her he loves her, but Brennan being Brennan just can't accept that although she loves him too. So the two of them spent a year apart and now she was going to tell him she loved him too, but then…you came along." Angela was trying to hide her anger because Sully really wasn't a bad guy, just a guy in a bad position.

Sully looked a bit hurt, but he understood. "I guess I've kind of expected this, he always really had the hots for his partner. I'll pack up and tell Temperance good-bye."

"Wow Sully, you really are an amazing guy," Angela said, "It might've been a different story if you had been her partner before Booth. But well…you know, thanks." And with that she walked away, mission accomplished.

Sully stood there for a moment and let the conversation sink in. Then he knew what he had to do. He headed back to Brennan's office.

"Temperance…" he said.

"What Sully," she asked, "I told you I'm busy."

"Yes but I've come to say good-bye," he said sadly.

"What?" Brennan asked sadly, but she was also kind of happy at the same time.

"I've been given another job far away," he lied, "I'll keep in touch though. It was nice to see you again."

Brennan got up from her desk and gave him a hug. "I'll miss you Sully."

"I'll miss you too," he said. That had been one of the hardest thing he had ever had to do, apart from leaving her the first time, but he knew he was leaving her in good hands.

He turned to leave the office and saw an upset Booth looking in from the window. Booth had slowly begun to walk away. Sully turned to Brennan, "You know, Booth's a good guy," he said, "I hear you should give him a chance." Then he left.

Brennan was startled, and then saw Booth through the window. She knew what she had to do.


	8. Finally

"Booth!" Brennan yelled as she practically ran out her office door.

He turned, "What Bones," he asked.

"Booth, I-, I need to talk to you," she said, "Can we go finish our coffee or something."

Booth wasn't sure what to expect. "Sure," he said.

Brennan flirtily grabbed his hand, something she definitely wasn't used to doing, and walked with him out the Jeffersonian.

* * *

They sat on the steps of the Lincoln Memorial instead because it had gotten dark out and the coffee cart had closed.

"So Bones, what did you…" Booth started to ask.

"Booth. I've been thinking," Brennan said promptly, staring directly into his eyes.

Booth started to get excited, but he didn't know what to expect, he had gotten his hopes up before. He just let her talk.

"Booth, I've been thinking. I've been let down by a lot of people in my life. I've been abandoned, and I've just never really known how… how someone could love me. But you've always been there for me. I've never really been able to process this thought, but I've finally been able to conclude…that…that I…" it was difficult for her to finish this, but she boldly said, "I love you Booth. I just hope I'm not too late."

Booth was grinning ear to ear. "Bones," he whispered as he got closer to her, "It'd never be too late. I couldn't get over you." He moved in slowly, and gently kissed her on the lips. "I love you," he said.

A tear fell down Brennan's cheek. She wanted to kiss him again, but more so she wanted him to hold her, hold her close and never let her go. She snuggled closely in his arms, wanting to freeze that moment forever.


End file.
